Locus 3871

Sequence ID dm3.chr2R
Location 8,499,892 – 8,500,039
Length 147
Max. P 0.997952
window5306 window5307 window5308 window5309 window5310

overview

Window 6

Location 8,499,892 – 8,499,996
Length 104
Sequences 4
Columns 105
Reading direction forward
Mean pairwise identity 77.94
Shannon entropy 0.35677
G+C content 0.40618
Mean single sequence MFE -26.85
Consensus MFE -18.30
Energy contribution -19.18
Covariance contribution 0.88
Combinations/Pair 1.22
Mean z-score -1.80
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.97
SVM RNA-class probability 0.864998
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 8499892 104 + 21146708
CCUUAUUUUUAAGGAUGUCUGGCGUUGCCAUCCUUAUUUG-AAGGAUGUAAGGCGUUGCCAACCUUAUUGCUAAGAAUGUGUAUUGACACACAUGAAUAGAAAUC
(((((....)))))..(..(((((.((((((((((.....-))))))....)))).)))))..)......(((...((((((......))))))...)))..... ( -29.00, z-score =  -2.78, R)
>droSim1.chr2R 6984470 104 + 19596830
-CCUUUUUCUAAGGAUAUACGGCGUUGCCAUCCUUAUUUUUAAGGACGUCAGGCGUUGCCGUCGUAAAUGCCAAGAAUGUGUUUUGACACACAUGUGUAGAGUUC
-.....(((((.((.(((((((((.((((.((((((....)))))).....)))).)))))).)))....))....((((((......))))))...)))))... ( -29.60, z-score =  -2.23, R)
>droSec1.super_1 6045996 105 + 14215200
CCUUUUUUCUAAGGAUAUACGGCGUUGCCAUCCUUAUUUUUAAGGACGUCAGGCGUUGCCGUCCUAAAUGCUAAGAAUGUGUAUUGACACACAUGUGUAGAGUUC
((((......))))....((((((.((((.((((((....)))))).....)))).))))))........(((...((((((......))))))...)))..... ( -30.60, z-score =  -2.78, R)
>droYak2.chr2R 12694936 103 - 21139217
CCUGAUUUCUAAGGAUUUCGGACGCUACCACUUUAUUUGUUAAGAAUGCCGGGUGUUGCCAUCACAAUUCCUAAG--UUUGUAUUGAUACACAUGUGUAGAAAUC
...((((((((((((.....((.((...((((((((((.....)))))..)))))..))..)).....))))...--..((((....))))......)))))))) ( -18.20, z-score =   0.58, R)
>consensus
CCUUAUUUCUAAGGAUAUACGGCGUUGCCAUCCUUAUUUUUAAGGACGUCAGGCGUUGCCAUCCUAAAUGCUAAGAAUGUGUAUUGACACACAUGUGUAGAAAUC
......(((((........(((((.(((((((((((....)))))))....)))).)))))...............((((((......))))))...)))))... (-18.30 = -19.18 +   0.88)

alignment

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secondary structure

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dotplot

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Window 7

Location 8,499,892 – 8,499,996
Length 104
Sequences 4
Columns 105
Reading direction reverse
Mean pairwise identity 77.94
Shannon entropy 0.35677
G+C content 0.40618
Mean single sequence MFE -25.52
Consensus MFE -17.66
Energy contribution -17.47
Covariance contribution -0.19
Combinations/Pair 1.36
Mean z-score -2.44
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.13
SVM RNA-class probability 0.983306
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 8499892 104 - 21146708
GAUUUCUAUUCAUGUGUGUCAAUACACAUUCUUAGCAAUAAGGUUGGCAACGCCUUACAUCCUU-CAAAUAAGGAUGGCAACGCCAGACAUCCUUAAAAAUAAGG
(((.(((....(((((((....))))))).....((..((((((.(....)))))))(((((((-.....)))))))))......))).)))((((....)))). ( -26.70, z-score =  -3.39, R)
>droSim1.chr2R 6984470 104 - 19596830
GAACUCUACACAUGUGUGUCAAAACACAUUCUUGGCAUUUACGACGGCAACGCCUGACGUCCUUAAAAAUAAGGAUGGCAACGCCGUAUAUCCUUAGAAAAAGG-
............(((((......)))))((((.((.((.....(((((...(((....(((((((....))))))))))...)))))..))))..)))).....- ( -26.70, z-score =  -2.48, R)
>droSec1.super_1 6045996 105 - 14215200
GAACUCUACACAUGUGUGUCAAUACACAUUCUUAGCAUUUAGGACGGCAACGCCUGACGUCCUUAAAAAUAAGGAUGGCAACGCCGUAUAUCCUUAGAAAAAAGG
......(((..(((((((....))))))).....((..(((((.((....)))))))((((((((....))))))))))......)))...((((......)))) ( -28.80, z-score =  -3.32, R)
>droYak2.chr2R 12694936 103 + 21139217
GAUUUCUACACAUGUGUAUCAAUACAAA--CUUAGGAAUUGUGAUGGCAACACCCGGCAUUCUUAACAAAUAAAGUGGUAGCGUCCGAAAUCCUUAGAAAUCAGG
((((((((....(((((....)))))..--...((((.......((....))..(((.((.((..((.......))...)).)))))...))))))))))))... ( -19.90, z-score =  -0.57, R)
>consensus
GAACUCUACACAUGUGUGUCAAUACACAUUCUUAGCAAUUAGGACGGCAACGCCUGACAUCCUUAAAAAUAAGGAUGGCAACGCCGGAUAUCCUUAGAAAAAAGG
((((.(((...(((((((....)))))))...))).))))...(((((...(((....((((((......)))))))))...))))).................. (-17.66 = -17.47 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 8

Location 8,499,928 – 8,500,035
Length 107
Sequences 4
Columns 108
Reading direction reverse
Mean pairwise identity 78.14
Shannon entropy 0.35612
G+C content 0.45496
Mean single sequence MFE -29.85
Consensus MFE -21.99
Energy contribution -23.92
Covariance contribution 1.94
Combinations/Pair 1.20
Mean z-score -3.13
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.22
SVM RNA-class probability 0.997952
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 8499928 107 - 21146708
UGCCACCCCCACCACAACACAUGUCG-GUGUUGCCAUACGGAUUUCUAUUCAUGUGUGUCAAUACACAUUCUUAGCAAUAAGGUUGGCAACGCCUUACAUCCUUCAAA
....................((((.(-(((((((((..(..(((.(((...(((((((....)))))))...))).)))..)..))))))))))..))))........ ( -29.70, z-score =  -3.12, R)
>droSim1.chr2R 6984506 103 - 19596830
UGCCAU----ACCUCAACACAUGUCG-GUGUUGCCAUACCGAACUCUACACAUGUGUGUCAAAACACAUUCUUGGCAUUUACGACGGCAACGCCUGACGUCCUUAAAA
......----..........((((((-((((((((.....(((..(((...((((((......))))))...)))..))).....))))))))).)))))........ ( -27.70, z-score =  -2.39, R)
>droSec1.super_1 6046033 107 - 14215200
UGCCAUCCCCACCUCAACACAUGUCG-GUGUUGCCAUACCGAACUCUACACAUGUGUGUCAAUACACAUUCUUAGCAUUUAGGACGGCAACGCCUGACGUCCUUAAAA
....................((((((-((((((((...(..((..(((...(((((((....)))))))...)))..))..)...))))))))).)))))........ ( -29.60, z-score =  -3.11, R)
>droYak2.chr2R 12694973 105 + 21139217
UGCCAUCUUAAUUCCAA-GUAGGUCGAGAGCUGCCAUCCCGAUUUCUACACAUGUGUAUCAAUACAAA--CUUAGGAAUUGUGAUGGCAACACCCGGCAUUCUUAACA
((((.((((....((..-...))..))))(.(((((((.(((((((((....(((((....)))))..--..))))))))).))))))).)....))))......... ( -32.40, z-score =  -3.90, R)
>consensus
UGCCAUCCCCACCUCAACACAUGUCG_GUGUUGCCAUACCGAACUCUACACAUGUGUGUCAAUACACAUUCUUAGCAAUUAGGACGGCAACGCCUGACAUCCUUAAAA
....................((((((.((((((((((...((((.(((...(((((((....)))))))...))).))))...)))))))))).))))))........ (-21.99 = -23.92 +   1.94)

alignment

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secondary structure

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dotplot

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Window 9

Location 8,499,933 – 8,500,039
Length 106
Sequences 4
Columns 107
Reading direction forward
Mean pairwise identity 77.78
Shannon entropy 0.36121
G+C content 0.46652
Mean single sequence MFE -33.02
Consensus MFE -24.24
Energy contribution -26.05
Covariance contribution 1.81
Combinations/Pair 1.21
Mean z-score -1.39
Structure conservation index 0.73
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.55
SVM RNA-class probability 0.740305
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 8499933 106 + 21146708
AGGAUGUAAGGCGUUGCCAACCUUAUUGCUAAGAAUGUGUAUUGACACACAUGAAUAGAAAUCCGUAUGGCAACAC-CGACAUGUGUUGUGGUGGGGGUGGCAACUA
............((((((..........(((...((((((......))))))...)))..((((.(((.(((((((-......))))))).))).)))))))))).. ( -35.40, z-score =  -2.08, R)
>droSim1.chr2R 6984511 102 + 19596830
AGGACGUCAGGCGUUGCCGUCGUAAAUGCCAAGAAUGUGUUUUGACACACAUGUGUAGAGUUCGGUAUGGCAACAC-CGACAUGUGUUGAGGU----AUGGCAUCUA
.(((.((((.((((((((((((....(((.....((((((......))))))..))).....))..))))))))..-((((....))))..))----.)))).))). ( -29.00, z-score =   0.14, R)
>droSec1.super_1 6046038 106 + 14215200
AGGACGUCAGGCGUUGCCGUCCUAAAUGCUAAGAAUGUGUAUUGACACACAUGUGUAGAGUUCGGUAUGGCAACAC-CGACAUGUGUUGAGGUGGGGAUGGCAUCUA
.(((.((((((.((((((((.(..(((.(((...((((((......))))))...))).)))..).)))))))).)-)..(((.(....).)))....)))).))). ( -35.10, z-score =  -1.22, R)
>droYak2.chr2R 12694978 104 - 21139217
AGAAUGCCGGGUGUUGCCAUCACAAUUCCUAAG--UUUGUAUUGAUACACAUGUGUAGAAAUCGGGAUGGCAGCUCUCGACCUAC-UUGGAAUUAAGAUGGCAACUC
............(((((((((..((((((.(((--(..(((((..((((....))))..)))(((((.......)))))))..))-))))))))..))))))))).. ( -32.60, z-score =  -2.40, R)
>consensus
AGGACGUCAGGCGUUGCCAUCCUAAAUGCUAAGAAUGUGUAUUGACACACAUGUGUAGAAAUCGGUAUGGCAACAC_CGACAUGUGUUGAGGUGGGGAUGGCAACUA
.((((((((...((((((((.((.(((.(((...((((((......))))))...))).))).)).))))))))...((((....)))).........)))))))). (-24.24 = -26.05 +   1.81)

alignment

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secondary structure

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dotplot

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Window 0

Location 8,499,933 – 8,500,039
Length 106
Sequences 4
Columns 107
Reading direction reverse
Mean pairwise identity 77.78
Shannon entropy 0.36121
G+C content 0.46652
Mean single sequence MFE -31.20
Consensus MFE -21.99
Energy contribution -23.92
Covariance contribution 1.94
Combinations/Pair 1.20
Mean z-score -3.08
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.09
SVM RNA-class probability 0.997389
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 8499933 106 - 21146708
UAGUUGCCACCCCCACCACAACACAUGUCG-GUGUUGCCAUACGGAUUUCUAUUCAUGUGUGUCAAUACACAUUCUUAGCAAUAAGGUUGGCAACGCCUUACAUCCU
..((((............))))..((((.(-(((((((((..(..(((.(((...(((((((....)))))))...))).)))..)..))))))))))..))))... ( -31.20, z-score =  -3.25, R)
>droSim1.chr2R 6984511 102 - 19596830
UAGAUGCCAU----ACCUCAACACAUGUCG-GUGUUGCCAUACCGAACUCUACACAUGUGUGUCAAAACACAUUCUUGGCAUUUACGACGGCAACGCCUGACGUCCU
(((((((((.----.............(((-((((....))))))).........((((((......))))))...))))))))).((((.((.....)).)))).. ( -28.90, z-score =  -2.30, R)
>droSec1.super_1 6046038 106 - 14215200
UAGAUGCCAUCCCCACCUCAACACAUGUCG-GUGUUGCCAUACCGAACUCUACACAUGUGUGUCAAUACACAUUCUUAGCAUUUAGGACGGCAACGCCUGACGUCCU
........................((((((-((((((((...(..((..(((...(((((((....)))))))...)))..))..)...))))))))).)))))... ( -29.60, z-score =  -2.51, R)
>droYak2.chr2R 12694978 104 + 21139217
GAGUUGCCAUCUUAAUUCCAA-GUAGGUCGAGAGCUGCCAUCCCGAUUUCUACACAUGUGUAUCAAUACAAA--CUUAGGAAUUGUGAUGGCAACACCCGGCAUUCU
..(((((((((.(((((((..-((((((((.((.......)).))))..))))...(((((....)))))..--....))))))).)))))))))............ ( -35.10, z-score =  -4.27, R)
>consensus
UAGAUGCCAUCCCCACCUCAACACAUGUCG_GUGUUGCCAUACCGAACUCUACACAUGUGUGUCAAUACACAUUCUUAGCAAUUAGGACGGCAACGCCUGACAUCCU
........................((((((.((((((((((...((((.(((...(((((((....)))))))...))).))))...)))))))))).))))))... (-21.99 = -23.92 +   1.94)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:18:26 2011